A: Bontoxilysin A C: Bontoxilysin A E: Bontoxilysin A B: Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH D: Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH F: Botulinum neurotoxin type E, nontoxic-nonhemagglutinin component, NTNH hetero molecules
Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has protein modification
Y
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION
-
Sample preparation
Crystal
Density Matthews: 3.77 Å3/Da / Density % sol: 67 % / Description: Three hetero-dimers per asymmetric unit
Crystal grow
Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 5.0ul sample was equilibrated against 600ul of 6 - 8% PEG 4000 and 0.1M sodium acetate of pH 4.6
Resolution: 3.05→49.3 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.872 / SU B: 38.792 / SU ML: 0.597 / Cross valid method: THROUGHOUT / ESU R Free: 0.762 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.32083
1334
1 %
RANDOM
Rwork
0.24338
-
-
-
obs
0.24415
133607
59.72 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 134.999 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.03 Å2
1.03 Å2
0 Å2
2-
-
1.03 Å2
0 Å2
3-
-
-
-3.33 Å2
Refinement step
Cycle: 1 / Resolution: 3.05→49.3 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
56949
0
3
0
56952
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.02
58077
X-RAY DIFFRACTION
r_bond_other_d
0.005
0.02
54825
X-RAY DIFFRACTION
r_angle_refined_deg
1.438
1.943
78768
X-RAY DIFFRACTION
r_angle_other_deg
0.94
3
125793
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.841
5
6987
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.42
25.962
2994
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.734
15
10098
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.001
15
150
X-RAY DIFFRACTION
r_chiral_restr
0.073
0.2
8820
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
66846
X-RAY DIFFRACTION
r_gen_planes_other
0.004
0.02
13842
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
12.49
12.484
28128
X-RAY DIFFRACTION
r_mcbond_other
12.488
12.484
28127
X-RAY DIFFRACTION
r_mcangle_it
19.914
18.634
35055
X-RAY DIFFRACTION
r_mcangle_other
19.914
18.634
35056
X-RAY DIFFRACTION
r_scbond_it
12.958
14.203
29949
X-RAY DIFFRACTION
r_scbond_other
12.957
14.203
29950
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_scangle_other
21.831
20.704
43714
X-RAY DIFFRACTION
r_long_range_B_refined
30.731
70663
X-RAY DIFFRACTION
r_long_range_B_other
30.731
70664
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05
Ens-ID
Dom-ID
Auth asym-ID
Number
1
1
A
78703
1
2
C
78703
2
1
A
78715
2
2
E
78715
3
1
C
78710
3
2
E
78710
4
1
B
70289
4
2
D
70289
5
1
B
70269
5
2
F
70269
6
1
D
70301
6
2
F
70301
LS refinement shell
Resolution: 3.05→3.133 Å
Rfactor
Num. reflection
% reflection
Rwork
0.673
3
-
Rfree
-
0
-
obs
-
-
0.02 %
+
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